[BioC] Rgraphviz in windows 7 - problem with GUI?

[Fraser Sim]

Hi Grace,

It looks like you're using an old version of R. You should upgrade to
2.12.1.

What version of graphviz do you have installed? What happens when you run
"library(Rgraphviz)"?

Cheers,
Fraser

-----Original Message-----
From: bioconductor-bounces at r-project.org
[mailto:bioconductor-bounces at r-project.org] On Behalf Of zhiqun tang
Sent: Monday, December 27, 2010 2:02 AM
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Rgraphviz in windows 7 - problem with GUI?

Hi, I got the similar problem when I run the KEGGgraph package. Below is the
detailed information. please note that I use 64-bit windows 7

I run the following codes:

mapkKGML <- system.file("extdata/hsa04010.xml",
package="KEGGgraph")





###################################################

### chunk number 4: parsemapk

###################################################

mapkG <- parseKGML2Graph(mapkKGML,expandGenes=TRUE)

mapkG





###################################################

### chunk number 5: parsemapk2

###################################################

mapkpathway <- parseKGML(mapkKGML)

mapkpathway

mapkG2 <- KEGGpathway2Graph(mapkpathway, expandGenes=TRUE)

mapkG2





###################################################

### chunk number 6: nodeandedge

###################################################

mapkNodes <- nodes(mapkG)

nodes(mapkG)[1:3]

mapkEdges <- edges(mapkG)

edges(mapkG)[1]





###################################################

### chunk number 7: keggnodedata

###################################################

mapkGnodedata <- getKEGGnodeData(mapkG)

mapkGnodedata[[2]]





###################################################

### chunk number 8: keggnodedataalt eval=FALSE

###################################################

## getKEGGnodeData(mapkG, 'hsa:5924')





###################################################

### chunk number 9: keggedgedata

###################################################

mapkGedgedata <- getKEGGedgeData(mapkG)

mapkGedgedata[[4]]





###################################################

### chunk number 10: keggedgedataalt eval=FALSE

###################################################

## getKEGGedgeData(mapkG,'hsa:627~hsa:4915')





###################################################

### chunk number 11: inout

###################################################

mapkGoutdegrees <- sapply(edges(mapkG), length)

mapkGindegrees <- sapply(inEdges(mapkG), length)

topouts <- sort(mapkGoutdegrees, decreasing=T)

topins <- sort(mapkGindegrees, decreasing=T)

topouts[1:3]

topins[1:3]





###################################################

### chunk number 12: subsetprepare

###################################################

library(Rgraphviz)

set.seed(123)

randomNodes <- sample(nodes(mapkG), 25)

mapkGsub <- subGraph(randomNodes, mapkG)

mapkGsub





###################################################

### chunk number 13: makeattr

###################################################

makeAttr <- function(graph, default, valNodeList) {

  tmp <- nodes(graph)

  x <- rep(default, length(tmp)); names(x) <- tmp



  if(!missing(valNodeList)) {

    stopifnot(is.list(valNodeList))

    allnodes <- unlist(valNodeList)

    stopifnot(all(allnodes %in% tmp))

    for(i in seq(valNodeList)) {

      x[valNodeList[[i]]] <- names(valNodeList)[i]

    }

  }

  return(x)

}





###################################################

### chunk number 14: subsetplot

###################################################

outs <- sapply(edges(mapkGsub), length) > 0

ins <- sapply(inEdges(mapkGsub), length) > 0

ios <- outs | ins



## translate the KEGG IDs into Gene Symbol

if(require(org.Hs.eg.db)) {

  ioGeneID <- translateKEGGID2GeneID(names(ios))

  nodesNames <- sapply(mget(ioGeneID, org.Hs.egSYMBOL, ifnotfound=NA),
"[[",1)

} else {

  nodesNames <- names(ios)

}

names(nodesNames) <- names(ios)



nAttrs <- list();

nAttrs$fillcolor <- makeAttr(mapkGsub, "lightgrey",
list(orange=names(ios)[ios]))

nAttrs$label <- nodesNames


Everything is fine so far, and the sessionInfo() is following:



R version 2.10.1 (2009-12-14)

i386-pc-mingw32



locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C


[5] LC_TIME=English_United States.1252



attached base packages:

[1] grid      stats     graphics  grDevices utils     datasets  methods
base



other attached packages:

[1] org.Hs.eg.db_2.3.6  RSQLite_0.8-4       DBI_0.2-5
AnnotationDbi_1.8.2
Biobase_2.6.1

[6] KEGGgraph_1.2.2     Rgraphviz_1.24.0    graph_1.26.0
XML_2.6-0




loaded via a namespace (and not attached):

[1] tools_2.10.1



However when I run

plot(mapkGsub, "neato", nodeAttrs=nAttrs,

     attrs=list(node=list(fillcolor="lightgreen",

                  width="0.75", shape="ellipse"),

       edge=list(arrowsize="0.7")))




The R GUI stopped, and shows that:

R for windows GUI front-end has stopped working

A problem caused the program to stop working correctly. Windows will close
the program and notify you if a solution is available



Anybody can tell me why this happens and how to solve it?

Thanks,

Grace

On Sat, Dec 25, 2010 at 12:03 AM, Alessandro Magrini <
alessandro.magrini at hotmail.it> wrote:

> mmh no...I have 32-bit Windows 7.
>
> graphviz works correctly, I have installed the version suggested 
> (2.20.3.1)...
>
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